Sure, it’ll be fixed as part of UE-218079. I talked with the dev team about this today and we’re going to go with a different approach as part of that JIRA. Currently, all the control rig code is using FStackAttributeContainer, which requires compact bone indices. But we also have FMeshAttributeContainer which uses mesh bones instead. If we switch the control rig code over to using this attribute container type, all the issues that we’ve been discussing on this thread go away, since the existing code is getting the bone index from the mesh, and the bones will always exist in the mesh (even if they aren’t skinned at a certain LOD).
We’re aiming to get this into 5.6, so if you keep an eye on the JIRA, there should be an update soon.